The native integration (using the Storj native protocol) has many benefits like a high parallelism, a client-side encryption, has access to much more storage nodes than to gateway nodes and when you have a wide bandwidth, robust network and need speed (however, you need a pretty high bandwidth to be faster than using S3 protocol at the moment). So if your bandwidth is 100Mbps you likely will not have a difference in speed, if less, S3 might be faster, if more than 1Gbps, then libuplink might be faster. However, downloads from the network are usually faster with libuplink (again, if you have a good internet channel) due to a parallelism.
See